Multiple sequence alignment - TraesCS1D01G297000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G297000 chr1D 100.000 2924 0 0 1 2924 395103206 395100283 0.000000e+00 5400.0
1 TraesCS1D01G297000 chr1D 85.587 1901 200 34 757 2616 395078874 395077007 0.000000e+00 1925.0
2 TraesCS1D01G297000 chr1D 85.241 1870 189 40 796 2616 395410837 395409006 0.000000e+00 1844.0
3 TraesCS1D01G297000 chr1D 97.494 838 11 2 1 829 395158931 395158095 0.000000e+00 1423.0
4 TraesCS1D01G297000 chr1D 78.165 1864 274 63 930 2734 395055398 395053609 0.000000e+00 1064.0
5 TraesCS1D01G297000 chr1D 83.954 698 78 20 2 675 395081464 395080777 3.180000e-179 638.0
6 TraesCS1D01G297000 chr1D 82.833 699 86 16 2 675 395413567 395412878 1.940000e-166 595.0
7 TraesCS1D01G297000 chr1D 76.923 182 29 7 407 586 395057264 395057094 1.120000e-14 91.6
8 TraesCS1D01G297000 chr1D 97.959 49 0 1 2876 2924 437471283 437471330 1.870000e-12 84.2
9 TraesCS1D01G297000 chr3D 94.160 1678 77 8 1 1669 57018556 57020221 0.000000e+00 2536.0
10 TraesCS1D01G297000 chr3D 96.369 1267 36 7 1664 2921 57021763 57023028 0.000000e+00 2076.0
11 TraesCS1D01G297000 chr3D 84.753 1843 211 36 812 2616 57035801 57037611 0.000000e+00 1783.0
12 TraesCS1D01G297000 chr3D 83.644 697 75 19 2 675 57034069 57034749 1.150000e-173 619.0
13 TraesCS1D01G297000 chr3D 100.000 28 0 0 2875 2902 517155677 517155704 5.000000e-03 52.8
14 TraesCS1D01G297000 chr1A 95.417 1593 64 4 544 2127 489361637 489360045 0.000000e+00 2529.0
15 TraesCS1D01G297000 chr1A 85.582 1942 191 38 707 2616 489394057 489392173 0.000000e+00 1953.0
16 TraesCS1D01G297000 chr1A 94.404 822 26 6 2119 2924 489357718 489356901 0.000000e+00 1245.0
17 TraesCS1D01G297000 chr1A 79.048 1890 273 67 788 2616 489325829 489324002 0.000000e+00 1182.0
18 TraesCS1D01G297000 chr1A 95.539 538 17 4 1 537 489377414 489376883 0.000000e+00 854.0
19 TraesCS1D01G297000 chr1A 83.144 706 76 15 2 686 489396307 489395624 3.220000e-169 604.0
20 TraesCS1D01G297000 chr1A 80.080 753 123 16 930 1665 489383738 489382996 4.290000e-148 534.0
21 TraesCS1D01G297000 chr1A 82.971 276 40 5 1 271 489338391 489338118 2.910000e-60 243.0
22 TraesCS1D01G297000 chr1B 86.650 2060 202 43 585 2616 526291819 526289805 0.000000e+00 2213.0
23 TraesCS1D01G297000 chr1B 77.933 2003 288 84 788 2729 526272532 526270623 0.000000e+00 1109.0
24 TraesCS1D01G297000 chr1B 95.161 496 23 1 1 496 526292570 526292076 0.000000e+00 782.0
25 TraesCS1D01G297000 chr1B 83.273 275 40 4 1 270 526274877 526274604 6.260000e-62 248.0
26 TraesCS1D01G297000 chr7D 92.000 50 4 0 2875 2924 603015819 603015770 1.450000e-08 71.3
27 TraesCS1D01G297000 chr5D 100.000 29 0 0 2874 2902 483824346 483824374 1.000000e-03 54.7
28 TraesCS1D01G297000 chr5D 100.000 28 0 0 2875 2902 390356963 390356990 5.000000e-03 52.8
29 TraesCS1D01G297000 chr6D 100.000 28 0 0 2875 2902 457474188 457474161 5.000000e-03 52.8
30 TraesCS1D01G297000 chr3A 96.875 32 0 1 2872 2902 144534011 144533980 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G297000 chr1D 395100283 395103206 2923 True 5400.0 5400 100.0000 1 2924 1 chr1D.!!$R1 2923
1 TraesCS1D01G297000 chr1D 395158095 395158931 836 True 1423.0 1423 97.4940 1 829 1 chr1D.!!$R2 828
2 TraesCS1D01G297000 chr1D 395077007 395081464 4457 True 1281.5 1925 84.7705 2 2616 2 chr1D.!!$R4 2614
3 TraesCS1D01G297000 chr1D 395409006 395413567 4561 True 1219.5 1844 84.0370 2 2616 2 chr1D.!!$R5 2614
4 TraesCS1D01G297000 chr1D 395053609 395057264 3655 True 577.8 1064 77.5440 407 2734 2 chr1D.!!$R3 2327
5 TraesCS1D01G297000 chr3D 57018556 57023028 4472 False 2306.0 2536 95.2645 1 2921 2 chr3D.!!$F2 2920
6 TraesCS1D01G297000 chr3D 57034069 57037611 3542 False 1201.0 1783 84.1985 2 2616 2 chr3D.!!$F3 2614
7 TraesCS1D01G297000 chr1A 489356901 489361637 4736 True 1887.0 2529 94.9105 544 2924 2 chr1A.!!$R5 2380
8 TraesCS1D01G297000 chr1A 489392173 489396307 4134 True 1278.5 1953 84.3630 2 2616 2 chr1A.!!$R6 2614
9 TraesCS1D01G297000 chr1A 489324002 489325829 1827 True 1182.0 1182 79.0480 788 2616 1 chr1A.!!$R1 1828
10 TraesCS1D01G297000 chr1A 489376883 489377414 531 True 854.0 854 95.5390 1 537 1 chr1A.!!$R3 536
11 TraesCS1D01G297000 chr1A 489382996 489383738 742 True 534.0 534 80.0800 930 1665 1 chr1A.!!$R4 735
12 TraesCS1D01G297000 chr1B 526289805 526292570 2765 True 1497.5 2213 90.9055 1 2616 2 chr1B.!!$R2 2615
13 TraesCS1D01G297000 chr1B 526270623 526274877 4254 True 678.5 1109 80.6030 1 2729 2 chr1B.!!$R1 2728

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
924 5604 1.515020 CTCGCTCCTCTTGGTCCTG 59.485 63.158 0.00 0.0 34.23 3.86 F
1566 6302 0.526524 CTAGTTGGAGCTCTTCGGCG 60.527 60.000 14.64 0.0 37.29 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 8145 0.179094 TGTCCACGACACAACTCCAC 60.179 55.0 0.0 0.0 37.67 4.02 R
2679 11386 0.884259 TGTGATCCACGCACAACAGG 60.884 55.0 0.0 0.0 42.75 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 214 3.428180 CCGATGACACACCTACAAGAGAG 60.428 52.174 0.00 0.00 0.00 3.20
482 672 2.202756 GTGGGCTAACGAGAGCGG 60.203 66.667 7.12 0.00 43.83 5.52
874 5546 1.523758 ATCAAAACTGTCAGCGGACC 58.476 50.000 14.62 0.00 43.65 4.46
924 5604 1.515020 CTCGCTCCTCTTGGTCCTG 59.485 63.158 0.00 0.00 34.23 3.86
1100 5802 4.896829 CCGCTCCTCCCTCGCCTA 62.897 72.222 0.00 0.00 0.00 3.93
1178 5883 2.438434 CCGAACACCTCCCATGCC 60.438 66.667 0.00 0.00 0.00 4.40
1180 5885 1.622607 CCGAACACCTCCCATGCCTA 61.623 60.000 0.00 0.00 0.00 3.93
1320 6025 2.033550 CCTCCTTCGGTACTTCGATGAG 59.966 54.545 5.16 10.02 39.03 2.90
1321 6026 2.022195 TCCTTCGGTACTTCGATGAGG 58.978 52.381 5.16 7.22 38.08 3.86
1322 6027 2.022195 CCTTCGGTACTTCGATGAGGA 58.978 52.381 5.16 0.00 38.66 3.71
1323 6028 2.623889 CCTTCGGTACTTCGATGAGGAT 59.376 50.000 5.16 0.00 38.66 3.24
1324 6029 3.551046 CCTTCGGTACTTCGATGAGGATG 60.551 52.174 5.16 0.24 38.66 3.51
1325 6030 2.927028 TCGGTACTTCGATGAGGATGA 58.073 47.619 5.16 0.00 33.92 2.92
1345 6056 1.496001 AGGATATGCCATTGCTGGTCA 59.504 47.619 0.00 0.00 45.10 4.02
1422 6133 3.744559 GCAAGGTCGTTTGCCTCA 58.255 55.556 9.74 0.00 45.93 3.86
1491 6227 0.709467 CATTCCGCGTCGTTTTCGTA 59.291 50.000 4.92 0.00 44.46 3.43
1566 6302 0.526524 CTAGTTGGAGCTCTTCGGCG 60.527 60.000 14.64 0.00 37.29 6.46
1597 6333 4.062293 TGTTGGTACGTTTGAGGATGAAG 58.938 43.478 0.00 0.00 0.00 3.02
1620 6359 5.069781 AGTCTATTTCTCCATGCCTAGTGTC 59.930 44.000 0.00 0.00 0.00 3.67
1767 8062 1.875576 GCCAGCGACAATCCTATCCTG 60.876 57.143 0.00 0.00 0.00 3.86
1794 8089 1.684734 GGAAGACGGTAGGCTGGGA 60.685 63.158 0.00 0.00 34.63 4.37
1817 8112 3.013921 TCGCACACCTGTTCTTTTTCTT 58.986 40.909 0.00 0.00 0.00 2.52
1832 8127 1.546961 TTCTTCCTCTCCGTCTGGTC 58.453 55.000 0.00 0.00 36.30 4.02
1885 8180 1.272490 GGACACAACGGAGAGACATCA 59.728 52.381 0.00 0.00 0.00 3.07
2056 8356 3.869623 CAAGCTGTGCCTACATCCT 57.130 52.632 0.00 0.00 35.97 3.24
2538 11215 8.383318 TGGATGTTTTTGTTTTTCAAAGTTCA 57.617 26.923 0.00 0.00 45.14 3.18
2911 11620 2.783510 CCCTGGTACTCCCCAAACATAT 59.216 50.000 0.00 0.00 33.07 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
482 672 3.521560 TCACGTGCATCTCTCCATTTAC 58.478 45.455 11.67 0.00 0.00 2.01
824 5457 6.488769 TTTCACACTCCAGTCCTTTAACTA 57.511 37.500 0.00 0.00 0.00 2.24
874 5546 2.508891 GGCGCGTCTCACAAGATCG 61.509 63.158 8.43 0.00 35.09 3.69
924 5604 2.804527 GTGTTAGGGTTTCGAGTTGGAC 59.195 50.000 0.00 0.00 0.00 4.02
1178 5883 1.064946 CAGTCGCGGAGGAAGCTAG 59.935 63.158 6.13 0.00 0.00 3.42
1180 5885 3.764466 CCAGTCGCGGAGGAAGCT 61.764 66.667 6.13 0.00 0.00 3.74
1320 6025 2.753452 CAGCAATGGCATATCCTCATCC 59.247 50.000 0.00 0.00 44.61 3.51
1321 6026 2.753452 CCAGCAATGGCATATCCTCATC 59.247 50.000 0.00 0.00 44.61 2.92
1322 6027 2.109480 ACCAGCAATGGCATATCCTCAT 59.891 45.455 0.00 0.00 44.61 2.90
1323 6028 1.496001 ACCAGCAATGGCATATCCTCA 59.504 47.619 0.00 0.00 44.61 3.86
1324 6029 2.157738 GACCAGCAATGGCATATCCTC 58.842 52.381 0.00 0.00 44.61 3.71
1325 6030 1.496001 TGACCAGCAATGGCATATCCT 59.504 47.619 0.00 0.00 44.61 3.24
1422 6133 1.079543 GTCCGCAGCACAGATCACT 60.080 57.895 0.00 0.00 0.00 3.41
1566 6302 0.037975 ACGTACCAACATCGGTGACC 60.038 55.000 0.65 0.00 40.39 4.02
1597 6333 5.283457 ACACTAGGCATGGAGAAATAGAC 57.717 43.478 0.00 0.00 0.00 2.59
1767 8062 0.979187 TACCGTCTTCCCCCACCATC 60.979 60.000 0.00 0.00 0.00 3.51
1794 8089 3.632145 AGAAAAAGAACAGGTGTGCGATT 59.368 39.130 0.00 0.00 0.00 3.34
1817 8112 1.078356 CTCGACCAGACGGAGAGGA 60.078 63.158 0.00 0.00 37.13 3.71
1850 8145 0.179094 TGTCCACGACACAACTCCAC 60.179 55.000 0.00 0.00 37.67 4.02
1885 8180 2.172679 GGGAAGAAGAGTCTCGAGGTT 58.827 52.381 13.56 0.32 30.70 3.50
2056 8356 6.392842 AGGGAAAGAGGGTCCATTTGATATTA 59.607 38.462 0.00 0.00 36.83 0.98
2538 11215 4.467438 CCTGCTTAAATGGAATCAGGGTTT 59.533 41.667 0.00 0.00 38.51 3.27
2679 11386 0.884259 TGTGATCCACGCACAACAGG 60.884 55.000 0.00 0.00 42.75 4.00


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.